Elliott Marcus, the city health department’s associate commissioner for food safety, said the cafe/takeout shop at 120 West Broadway was reinspected on Monday and again assessed 80 points. A passing score is 28 points or under.

And a Nov. 24 inspection of the flagship restaurant Bouley, down the street at 163 Duane Street, found 50 violations worth 50 points. It, too, will be reinspected.

Among the violations found on Nov. 5 at the bakery/cafe were “sewage disposal system in disrepair or not functioning properly,” “toilet facility not maintained and provided with toilet paper,” “harborage or conditions conducive to vermin infestation exist,” “hand washing facility not provided in or near food preparation area and toilet room,” “evidence of, or flying insects in facility’s food and/ or non-food areas” and “evidence of, or live mice in facility’s food and/ or non-food areas.”

In a telephone interview on Tuesday, before the health department released the second inspection report, Mr. Bouley said, “We’ve repaired everything.” He said work on a water main outside might have led to some of the rodent problems, but “our exterminator has been in there every day since.”

Many of the violations in Monday’s inspection involved food for sale on counters and at steam tables in Bouley Bakery and Market’s self-serve area, but an inspector also found “approximately 60 mouse excreta observed on floor inside the main frame electrical room, located in the rear of the pastry area, in the basement;” “9 live house flies” on the premises; spelt flour “contaminated by 1 live bug in a storage container;” five full trash cans without tight-fitting lids in the garbage storage room in the basement; and deli slicers “dirty with old food debris.”

And at Bouley, inspectors on Nov. 24 found “3 quart containers of G.A.F. Seeling Cultured Reduced Fat Buttermilk observed with an expiration date of 11/12/09,” “3 quart containers of G.A.F. Seeling whole milk observed with an expiration date of 11/21/09,” “one partially used bottle of ready-to-drink Cinzano Extra Dry Vermouth observed to be contaminated by fruit flies” and “approximately 50 pound(s) of ice for customer consumption observed to be contaminated by mold growth in the water compartment of the ice machine.”

“We take this seriously,” Mr. Bouley said today. “We don’t want this to ever happen again.” He said he had hired a former health department official to help set up better procedures. For instance, if food is left out to be served at the cafe, log books need to record how long it’s been out. “We’re putting a better structure in to take care of it.’’

As for the flies at the market, he said, “We must have 300 baby carriages a day through those doors. Now we have to keep the doors closed and we have to assist people with baby carriages to open the doors.’’

He said the restaurant needed to be more careful about things like outdated milk, but he also said inspectors are “going around generating as much points and income as possible. I’ve never seen anything like this.”

On Nov. 24, the health inspector also shut down the flagship restaurant’s sous vide equipment after she found that it was being used without an approved safety plan.

“We’ve been asking him to give us one for a long time,” Mr. Marcus said. “At least two years ago, maybe longer.”

Since 2006, the health department has cracked down on restaurants’ use of sous vide — cooking vacuum-sealed food at low temperatures. It requires anyone using the equipment to have an approved Hazard Analysis and Critical Control Point, or HACCP, plan. Thirty-one restaurants in the city have had plans approved, but not Bouley.

At the time of the crackdown, Dana Bowen wrote, “Longtime practitioners of sous vide, like the chef David Bouley, say that they have always kept the kind of documentation the city is looking for — records outlining temperatures used and the amount of time food is stored — and that more recent converts should, too. ‘I think it’s a good thing,’ Mr. Bouley said of the new requirements.”

Mr. Bouley said today that his restaurants had stopped using sous vide years ago and had only resumed it when Shea Gallante took charge of the kitchen at Bouley in June. He said Mr. Gallante had submitted an HACCP plan three months ago.